Physiological role of acylated ghrelin (AG), unacylated ghrelin (UAG) and obestatin is poorly understood especially in childhood. To understand their biological implications in obesity and metabolic syndrome (MS), we measured AG, UAG, obestatin, at fasting and every 60′ during oral glucose tolerance test (OGTT) in 60 prepubertal (PPOB; 32) and pubertal (P-OB; 28) children. Paediatric IDF 2007 criteria was used to identifying MS. In PP-OB group, 20 (62.5%) children had MS and four of them had glucose intolerance (impaired fasting glucose or impaired glucose tolerance). In P-OB group, 28 (100%) children had MS and five had glucose intolerance. UAG (P<0.004), obestatin (P<0.05) were lower in OB-P when compared to OB-PP. AG levels were higher in both prepubertal and pubertal males when compared to females (P<0.04). During OGTT: i) AG levels decreased at 60 min (P<0.04) and returned to basal levels at 120 min in both PP-OB and P-OB; ii) UAG levels decreased for all the testing session (P<0.0001) in both groups and more significantly in PP-OB when compared to P-OB (P<0.02); iii) obestatin levels decreased at 120 min (P<0.04) in both groups. Fasting UAG (P<0.01) and during OGTT obestatin levels (P<0.01) were higher in children with MS when compared to those without MS. Fasting UAG (P<0.05) and obestatin (P<0.02) were lower in PP-OB children with glucose intolerance when compared to euglycemic PP-OB. The levels of three peptides were positively correlated each others (P<0.004). The AG decrease was correlated with glucose nadir during OGTT (r: 0.357; P<0.02). The UAG decrease was associated with fasting insulin, HOMA index and insulin nadir (r: 0.372; P<0.02) during OGTT. The obestatin decrease was associated with fasting HDL-cholesterol (r: −0.497; P<0.002). In conclusion AG, UAG and obestatin were differently inhibited during OGTT in OB children. MS influences the glucose-induced regulation of ghrelin system in childhood.